Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA.
Int J Mol Sci. 2020 Jul 8;21(14):4826. doi: 10.3390/ijms21144826.
The comparison of the landscape of somatic alterations in circulating tumor cells (CTCs) versus metastases is challenging. Here, we comprehensively characterized the somatic landscape in bulk (amplified and non-amplified), spike-in breast cancer cells, CTCs, and metastases from breast cancer patients using whole-exome sequencing (WES). We determined the level of genomic concordance for somatic nucleotide variants (SNVs), copy number alterations (CNAs), and structural variants (SVs). The variant allele fractions (VAFs) of somatic variants were remarkably similar between amplified and non-amplified cell line samples as technical replicates. In clinical samples, a significant fraction of somatic variants had low VAFs in CTCs compared to metastases. The most frequently recurrent gene mutations in clinical samples were associated with an elevated C > T mutational signature. We found complex rearrangement patterns including intra- and inter-chromosomal rearrangements, singleton, and recurrent gene fusions, and tandem duplications. We observed high molecular discordance for somatic alterations between paired samples consistent with marked heterogeneity of the somatic landscape. The most prevalent copy number calls were focal deletion events in CTCs and metastases. Our results demonstrate the feasibility of an integrated workflow for the identification of a complete repertoire of somatic alterations and highlight the intrapatient genomic differences that occur between CTCs and metastases.
比较循环肿瘤细胞 (CTC) 和转移灶中的体细胞改变的图谱具有挑战性。在这里，我们使用全外显子组测序 (WES) 全面表征了大量 (扩增和非扩增)、掺入乳腺癌细胞、CTC 和乳腺癌患者转移灶中的体细胞图谱。我们确定了体细胞核苷酸变异 (SNV)、拷贝数改变 (CNA) 和结构变异 (SV) 的基因组一致性水平。作为技术重复，扩增和非扩增细胞系样本中的体细胞变异的等位基因变异分数 (VAF) 非常相似。在临床样本中，与转移灶相比，CTC 中的体细胞变异的 VAF 有相当一部分较低。临床样本中最常出现的基因突变与 C > T 突变特征升高有关。我们发现了复杂的重排模式，包括染色体内和染色体间重排、单峰和复发性基因融合以及串联重复。我们观察到配对样本之间的体细胞改变存在高度的分子不一致性，这与体细胞图谱的明显异质性一致。最常见的拷贝数调用是 CTC 和转移灶中的局灶性缺失事件。我们的结果证明了用于鉴定完整的体细胞改变谱的集成工作流程的可行性，并强调了 CTC 和转移灶之间发生的患者内基因组差异。
